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Maven jandex plugin does not generate index for local custom maven repositories (sometimes)

I have a multi module maven project wie quarkus modules and some custom libraries which are local maven repositories (so they can be used by the other maven projects/modules). However, so that local maven repositories are recognizable und usable by your other local maven projects, you have to manually index them for some reason. I.e. add a config like this for quarkus index to the application.properties of the project including the local maven repo dependency:
quarkus.index-dependency.<index-name>.group-id = <group-id-of-local-maven-repo>
quarkus.index-dependency.<index-name>.artifact-id = <artifact-id-of-local-maven-repo>
The problem is, this causes issues for me becausse if you have 3 layers of project dependencies, say:
Project A (custom local maven repo library)
Project B (custom local maven repo library, includes Project A dependency)
application.properties (indexing Project A library dependency)
Project C (Local maven project for an end product, includes Project B
library dependency - and through it indirectly Project A).
application.properties (indexing Project B library dependency and config for datasources or other app related things)
Then when you generate an uber-jar (fat jar) of Project C for deployment, it for some reason uses application.properties of Project B in the packaged jar, instead of from the project which im building (Project C). Thus, the app is missing key configs and does not work. Maven seems to use an inverse priority here, which i dont know if thats a bug or not. When i asked about this, i was simply told that:
"My dependencies should not have application.properties".
I tried to find a way to prevent manual indexing via application.properties and found the maven jandex plugin - which is supposed to generate an index. The next problem is, this seems to only work in some projects but not in others in the dependency hierarchy, resulting in the same situation as before, and i don't understand why. This is the pom.xml config for the plugin i have included in all 3 projects (the entire pom.xml for all is too long, so let me know if you need more info):
<properties>
...
<jandex.skip>false</jandex.skip>
...
</properties>
...
<build>
...
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.5</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
<configuration>
<skip>${jandex.skip}</skip>
</configuration>
</plugin>
...
The odd thing is, this works to the extend that i no longer have to index Project B library dependency in Project C application.properties, but Project B library dependency still has to manually index Project A library dependency - thus rendering the entire exercise futile. Project C having an application.properties was never the issue, and is obviously needed. Project B still requires a properties file to point to Project A now, how do i solve this?
I have a parent module POM in the root folder containing all these projects, over which this maven jandex dependency is distributed to all modules, so it looks like this:
Maven parent module (contains all dependencies and versions used by all project sub modules)
Project A (custom local maven library repo), own pom.xml with inheritance from parent module
Project B (custom local maven library repo, includes Project A library), own pom.xml with inheritance from parent module
application.properties - Indexes Project A dependency manually, this is the problematic one which needs to go!
Project C (Local maven project for REST API etc., includes Project B library), own pom.xml with inheritance from parent module
pom.xml (parent module POM, containing maven jandex dependepency among others)
Edit: One of the projects, "entity", where all the database access objects are stored, does not run the jandex plugin during mvn clean install. This is the POM of the project:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.compamny.project</groupId>
<artifactId>entity</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-orm</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-validator</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-resteasy-reactive-jackson</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jdk8</artifactId>
<version>2.13.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.smallrye/jandex-maven-plugin -->
<dependency>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
When i force the execution of the jandex goal with mvn io.smallrye:jandex-maven-plugin:3.0.0:jandex it creates an META-INF/jandex.jdx file, but it does not produce one when i run mvn clean install. This is not a solution since i need to build the project, run the jandex plugin and install it into my local repositories separately. Also, notice that im using the "io.smallrye" version of the jandex plugin since the "org.jboss" version seems to not work at all.

I figured it out. The jandex plugin was set in the <pluginManagement> section of the POM configuration, which made it not run on mvn clean install. I had to move it to the plugins section so it gets executed. Thanks #Ladicek for making me look closer and keep trying!

Maven Shade plugin configuration to create uber jar containing just the submodules based in the same groupId

Having the following situation:
STS
Java
Maven
Machine One
workspace-01
the Java app with Maven is based for a single module.
It is installed (mvn install) in the repository and the master-project.jar file in other Machine is installed and used for other project how
<dependency>
<groupId>com.manuel.jordan</groupId>
<artifactId>master-project</artifactId>
<version>0.0.1.SNAPSHOT</version>
</dependency>
Until here all work fine
workspace-02
The app grew up and in other workspace the app was migrated to work with multi-modules
Lets assume the following structure for simplicity
master-project (<packaging>pom</packaging>)
alpha (<packaging>jar</packaging>)
beta (<packaging>jar</packaging>)
numbers (<packaging>pom</packaging>)
one (<packaging>jar</packaging>)
two (<packaging>jar</packaging>)
countries (<packaging>pom</packaging>)
Europe (<packaging>pom</packaging>)
France (<packaging>jar</packaging>)
Italy (<packaging>jar</packaging>)
AmericaLatina (<packaging>pom</packaging>)
Peru (<packaging>jar</packaging>)
Argentina (<packaging>jar</packaging>)
I am able to compile all these modules. Therefore build success
Goal
Now the goal is generate the same master-project.jar file including the sub modules how internal jars.
After to do a research the solution is: maven-shade-plugin
What is the maven-shade-plugin used for, and why would you want to relocate Java packages?
I have the following configuration (part of it) using how reference the following links and other sources:
Create JAR file as Aggregation in maven multi module package
Therefore:
<modelVersion>4.0.0</modelVersion>
<packaging>pom</packaging> <--- it is the main or root pom.xml file
<groupId>com.manuel.jordan</groupId>
<artifactId>master-project</artifactId>
<version>0.0.1-SNAPSHOT</version>
<properties>
....
</properties>
<dependencies>
<dependency>
<groupId>com.hazelcast</groupId>
<artifactId>hazelcast-all</artifactId>
<version>${hazelcast.version}</version>
<scope>provided</scope> <!-- Otherwise each uber jar within each submodule is 11.6MB -->
</dependency>
</dependencies>
<modules>
<module>...</module>
...
</modules>
<build>
<plugins>
....
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
<executions>
<execution>
<id>create-fat-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<artifactSet>
<includes>
<include>com.manuel.jordan</include>
</includes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
With the current configuration happens the following:
For each module within the target directory:
With <packaging>pom</packaging> generates a .pom file
With <packaging>jar</packaging> generates two .jar files, one of the sub module itself and other of the uber jar (yes for each module)
Goal: what is the extra or missing configuration to generate something like this:
master-project.jar containing
module1.jar
module2.jar
...
module3.jar
Where each module# have the same <groupId>com.manuel.jordan</groupId> declaration, that's why I declared
<configuration>
<artifactSet>
<includes>
<include>com.manuel.jordan</include>
</includes>
</artifactSet>
</configuration>
And observe that the root/main pom.xml file has <packaging>pom</packaging>
Goal
Therefore the goal is that the other project located in the other machine keeps in peace
<dependency>
<groupId>com.manuel.jordan</groupId>
<artifactId>master-project</artifactId>
<version>0.0.1.SNAPSHOT</version>
</dependency>
Thus it does not matter if the master-project project is either single or multi-module

You could make a packaging jar module below your master-project with a dependency to the other modules, and include only there the shade plugin configuration

Java 11 package is declared in module which does not export it

I have created two modular programs. One is JavaFX modular project that contains module-info.java like:
module checker {
requires javafx.fxml;
requires javafx.controls;
requires TextInputProgram; // Btw, IDEA shows me here "Ambiguous module reference"
exports sample;
opens sample;
}
Another Maven project that contains module-info.java like:
module TextInputProgram {
requires selenium.api;
requires selenium.chrome.driver;
}
So, I added modular maven project as external jar into JavaFX (via Project Structure in libs and in module-info via requires I specified jar). Also I added variable that contains external jar for compilation (in addition to PATH_TO_FX and PATH_TO_FX_MODS):
set EXTERNAL_JAR="...\out\artifacts\TextInputProgram_jar"
But when I'm trying to compile the project via command:
dir /s /b src\*.java > sources.txt & javac --module-path %EXTERNAL_JAR%;%PATH_TO_FX% -d mods/checker #sources.txt & del sources.txt
following this tutorial
I'm getting from JavaFX project class the error:
\src\sample\Controller.java:9: error: package project is not visible
import project.SeleniumProgram;
^
(package project is declared in module TextInputProgram, which does not export it)
1 error
Package is declared in module which does not export it
import project.SeleniumProgram I imported in JavaFX project to use classes from external jar.
Updated:
If I add exports project; inside module-info.java of maven project then I see the error in JavaFX module-info.java:
If I delete requires TextInputProgram; then I have another error from import:
Am I missing something here? I'm trying to get executable Jar of these two programs.

As discussed throughout the comments, there are a few possible issues here:
Module definition
Local jars and dependencies
Based on the modular projects posted, I'll create a small demo multi-modular project to explain both problems.
Maven multi-modular project
Using your IDE, create a Maven project, then add two modules, TextInputProgram and checker, like:
Parent pom
<groupId>org.openjfx</groupId>
<artifactId>hellofx</artifactId>
<version>1.0-SNAPSHOT</version>
<modules>
<module>TextInputProgram</module>
<module>checker</module>
</modules>
<packaging>pom</packaging>
TextInputProgram pom
<parent>
<groupId>org.openjfx</groupId>
<artifactId>hellofx</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>TextInputProgram</artifactId>
<properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<version>3.141.59</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<release>11</release>
</configuration>
</plugin>
</plugins>
</build>
Module-info.java
module TextInputProgram {
requires selenium.api;
requires selenium.chrome.driver;
exports project to checker;
}
Checker pom
<parent>
<artifactId>testMods</artifactId>
<groupId>org.openjfx</groupId>
<version>1.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>checker</artifactId>
<dependencies>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-controls</artifactId>
<version>12.0.2</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-fxml</artifactId>
<version>12.0.2</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>TextInputProgram</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<release>11</release>
</configuration>
</plugin>
<plugin>
<groupId>org.openjfx</groupId>
<artifactId>javafx-maven-plugin</artifactId>
<version>0.0.3</version>
<configuration>
<mainClass>sample.Main</mainClass>
</configuration>
</plugin>
</plugins>
</build>
Module-info.java
module checker {
requires javafx.fxml;
requires javafx.controls;
requires TextInputProgram;
opens sample to javafx.fxml;
exports sample;
}
(Code of both modules is irrelevant at this point).
Solutions included
Now note that you have to add this in the TextInputProgram module descriptor:
exports project to checker;
if you want to let checker module to access TextInputProgram's project package.
This will solve this error:
package project is declared in module TextInputProgram, which does not export it
Also, note that I've included this dependency in the checker project:
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>TextInputProgram</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
Even having two modules, under the same parent, you need to include the dependency from one module to the other. Otherwise this will fail (module not found):
requires TextInputProgram;
You can run mvn clean install in the TextInputProgram module, to install org.openjfx:TextInputProgram:1.0-SNAPSHOT in your local repository .m2.
Then you can run mvn clean javafx:run int the checker module, to run the GUI project.
It is worth mentioning that it is not a good idea to combine both maven dependencies with jar files. If you end up using both, you will get this error:
Module 'checker' reads 'project' from both 'TextInputProgram' and 'TextInputProgram'
This message means that there are two modules in the module path with the exact same name, one the maven dependency, the other one, the jar artifact.
In order to distribute your project and modules, it is better to use the maven approach, and avoid having jar files in lib folders. Later on your modules will be published as separated artifacts, and you won't need to modify your pom files (other than to update the version numbers).

Classloader with Maven built jar

I am working on a project which contains a number of subprojects. The structure is something like Project 1, Project 2 and ProjectClassLoader.
Using separate configuration files, I pass in the binary names of the classes from Projects 1 and 2 that need to be loaded each time as arguments to the ProjectClassLoader project.
The ProjectClassLoader gets a handle to the system classloader
ClassLoader loader = ClassLoader.getSystemClassLoader();
which in theory allows it to load any classes which are contained in the classpath.
I'm using Maven to build the projects and handle their associated dependences. Thus each project has it's own individual pom.xml file. The ProjectClassLoader defines a parent pom.xml over Projects 1 and 2 which inherit from this. The parent pom contains dependency entries for both Project 1 and 2.
My understanding was that any dependencies specified in the pom.xml files of these projects would get added to the classpath at runtime. However when trying to load classes using the system classloader, I'm getting class not found execptions.
I have tried using the mvn:exec plugin which I understand includes the dependencies in the classpath when executing jars on the command line but this has not worked.
I'd grately appreciate any help in furthering my understanding of why I can load the classes even though the dependencies are defined in the pom...Thanks in advance

Can you check if your pom matches this configuration a bit?
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
...
<properties>
...
<exec.maven.plugin.version>1.2.1</exec.maven.plugin.version>
...
</properties>
<build>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
</plugin>
...
</plugins>
<pluginManagement>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>${exec.maven.plugin.version}</version>
<configuration>
<executable>java</executable>
<arguments>
<argument>-classpath</argument>
<!-- automatically creates the classpath using all project dependencies, also adding the project build directory -->
<classpath />
<argument>com.example.Main</argument><!-- your mainClass -->
</arguments>
</configuration>
</plugin>
...
</plugins>
</pluginManagement>
</build>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
</dependency>
...
</dependencies>
<dependencyManagement>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
<version>${project1.version}</version>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
<version>${project2.version}</version>
</dependency>
...
</dependencies>
</dependencyManagement>
...
</project>
Where you fill them with the correct artifacts.
You should then be able to start it with:
mvn exec:exec
Can you post your configuration for your pom plz if it doesn't match, that way it's easier to understand what exactly you currently have in your pom.

mvn generate-sources fails, why isn't xml beans on classpath?

I'm trying to generate java classes for OGC KML 2.2 as part of the maven generate-sources process using the org.codehaus.mojo xmlbeans-maven-plugin. The java code appears to be generated correctly, but I get tons of errors during compilation complaining that 'package org.apache.xmlbeans'. XMLBeans is clearly a dependency, it exists in my ~/.m2 repository, and I've been peek in the jar to make sure the classes are there. It looks like XMLBeans is successfully generating java files in target/generated-sources, but somehow its absent from the classpath during compilation.
I've tried changing the scope of the org.apache.xmlbeans dependency, but to no avail.
Here's the pom.xml
<modelVersion>4.0.0</modelVersion>
<groupId>net.opengis</groupId>
<artifactId>ogc-kml</artifactId>
<version>2.2.0</version>
<packaging>pom</packaging>
<name>ogc-kml</name>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>xmlbeans-maven-plugin</artifactId>
<version>2.3.3</version>
<executions>
<execution>
<goals>
<goal>xmlbeans</goal>
</goals>
</execution>
</executions>
<inherited>true</inherited>
<configuration>
<download>true</download>
<schemaDirectory>src/main/xsd</schemaDirectory>
</configuration>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.xmlbeans</groupId>
<artifactId>xmlbeans</artifactId>
<version>2.6.0</version>
</dependency>
</dependencies>
</dependencyManagement>
The project consists of a single src/main/xsd folder containing the two xsds from http://schemas.opengis.net/kml/2.2.0/. The entire folder structure is at https://github.com/iancw/maven-xmlbeans-question.
I can compile the classes by hand if I put the xmlbeans jar from my ~/.m2 repo on the classpath, e.g.
xmlbeans$ javac -classpath ~/.m2/repository/org/apache/xmlbeans/xmlbeans/2.4.0/xmlbeans-2.4.0.jar org/w3/x2005/atom/*.java org/w3/x2005/atom/impl/*.java net/opengis/kml/x22/*.java x0/oasisNamesTcCiqXsdschemaXAL2/*.java x0/oasisNamesTcCiqXsdschemaXAL2/impl/*.java net/opengis/kml/x22/*.java net/opengis/kml/x22/impl/*.java
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
xmlbeans$
I've looked through a number of examples and it seems like I'm doing this right. I haven't seen anyone else complain of this issue. Any maven mavens have suggestions?
(A curious side note is that although i've tried both 2.4.0 and 2.6.0 of the xmlbeans dependency, maven hasn't ever seemed to download the 2.6.0 version into my repository)

From the POM file that you've included in your question you have only defined the xmlbeans dependency in the dependencyManagement section. You also need to define it in your dependencies section of your POM before it will be included in the classpath at build time.
So for example your POM would be:
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>xmlbeans-maven-plugin</artifactId>
...
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.xmlbeans</groupId>
<artifactId>xmlbeans</artifactId>
<version>2.6.0</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<groupId>org.apache.xmlbeans</groupId>
<artifactId>xmlbeans</artifactId>
</dependencies>

One Additional issue that may look similar,
Check your java install jdk and ext folders for older beans jar.
The plugin puts the project dependencies at the end of the classpath.